David A. Stahl - Publications

Civil and Environmental Engineering University of Washington, Seattle, Seattle, WA 
 Northwestern University, Evanston, IL 
 University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Environmental microbiology, microbial evolution, microbial ecology, sulfate reducer, methanogen, syntrophy, ammonia oxidation, symbiosis

210 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Turkarslan S, Stopnisek N, Thompson AW, Arens CE, Valenzuela JJ, Wilson J, Hunt KA, Hardwicke J, de Lomana ALG, Lim S, Seah YM, Fu Y, Wu L, Zhou J, Hillesland KL, ... Stahl DA, et al. Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions. The Isme Journal. PMID 33612833 DOI: 10.1038/s41396-021-00919-9  0.76
2021 Wang Y, Qin W, Jiang X, Ju F, Mao Y, Zhang A, Stahl DA, Zhang T. Seasonal Prevalence of Ammonia-Oxidizing Archaea in a Full-Scale Municipal Wastewater Treatment Plant Treating Saline Wastewater Revealed by a 6-Year Time-Series Analysis. Environmental Science & Technology. PMID 33539079 DOI: 10.1021/acs.est.0c07703  0.4
2020 Qin W, Zheng Y, Zhao F, Wang Y, Urakawa H, Martens-Habbena W, Liu H, Huang X, Zhang X, Nakagawa T, Mende DR, Bollmann A, Wang B, Zhang Y, Amin SA, ... ... Stahl DA, et al. Alternative strategies of nutrient acquisition and energy conservation map to the biogeography of marine ammonia-oxidizing archaea. The Isme Journal. PMID 32636492 DOI: 10.1038/S41396-020-0710-7  1
2020 Wei SP, Stensel HD, Nguyen Quoc B, Stahl DA, Huang X, Lee PH, Winkler MH. Flocs in disguise? High granule abundance found in continuous-flow activated sludge treatment plants. Water Research. 179: 115865. PMID 32388048 DOI: 10.1016/J.Watres.2020.115865  0.4
2020 Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, Shi W, Wu L, Zhang Y, Yang Y, Adams BG, Rocha AM, Detienne BL, Lowe KA, Joyner DC, ... ... Stahl DA, et al. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. 8: 51. PMID 32252814 DOI: 10.1186/S40168-020-00825-W  0.32
2020 Zhang Y, Qin W, Hou L, Zakem EJ, Wan X, Zhao Z, Liu L, Hunt KA, Jiao N, Kao SJ, Tang K, Xie X, Shen J, Li Y, Chen M, ... ... Stahl DA, et al. Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean. Proceedings of the National Academy of Sciences of the United States of America. PMID 32071230 DOI: 10.1073/Pnas.1912367117  0.68
2019 Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown MR, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, ... ... Stahl DA, et al. Author Correction: Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology. PMID 31728072 DOI: 10.1038/S41564-019-0617-0  1
2019 Wang B, Qin W, Ren Y, Zhou X, Jung MY, Han P, Eloe-Fadrosh EA, Li M, Zheng Y, Lu L, Yan X, Ji J, Liu Y, Liu L, Heiner C, ... ... Stahl DA, et al. Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. The Isme Journal. PMID 31462715 DOI: 10.1038/S41396-019-0493-X  1
2019 Wu L, Ning D, Zhang B, Li Y, Zhang P, Shan X, Zhang Q, Brown M, Li Z, Van Nostrand JD, Ling F, Xiao N, Zhang Y, Vierheilig J, Wells GF, ... ... Stahl DA, et al. Global diversity and biogeography of bacterial communities in wastewater treatment plants. Nature Microbiology. PMID 31086312 DOI: 10.1038/S41564-019-0426-5  1
2018 Heal KR, Qin W, Amin SA, Devol AH, Moffett JW, Virginia Armbrust E, Stahl DA, Ingalls AE. Accumulation of NO -cobalamin in nutrient-stressed ammonia-oxidizing archaea and in the oxygen deficient zone of the Eastern Tropical North Pacific. Environmental Microbiology Reports. PMID 30022612 DOI: 10.1111/1758-2229.12664  0.68
2017 Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, ... ... Stahl DA, et al. Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. Mbio. 8. PMID 29138306 DOI: 10.1128/Mbio.01780-17  0.76
2017 Qin W, Amin SA, Lundeen RA, Heal KR, Martens-Habbena W, Turkarslan S, Urakawa H, Costa KC, Hendrickson EL, Wang T, Beck DA, Tiquia-Arashiro SM, Taub F, Holmes AD, Vajrala N, ... ... Stahl DA, et al. Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations. The Isme Journal. PMID 29053148 DOI: 10.1038/Ismej.2017.186  1
2017 Qin W, Heal KR, Ramdasi R, Kobelt JN, Martens-Habbena W, Bertagnolli AD, Amin SA, Walker CB, Urakawa H, Könneke M, Devol AH, Moffett JW, Armbrust EV, Jensen GJ, Ingalls AE, ... Stahl DA, et al. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology. PMID 29034851 DOI: 10.1099/Ijsem.0.002416  1
2017 Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, et al. Mechanism for microbial population collapse in a fluctuating resource environment. Molecular Systems Biology. 13: 919. PMID 28320772 DOI: 10.15252/Msb.20167058  0.76
2017 Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J. Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer. Environmental Science & Technology. PMID 28300407 DOI: 10.1021/Acs.Est.6B02980  0.32
2017 Qin W, Meinhardt KA, Moffett JW, Devol AH, Armbrust EV, Ingalls AE, Stahl DA. Influence of Oxygen Availability on the Activities of Ammonia-oxidizing Archaea. Environmental Microbiology Reports. PMID 28211189 DOI: 10.1111/1758-2229.12525  0.68
2016 Heal KR, Qin W, Ribalet F, Bertagnolli AD, Coyote-Maestas W, Hmelo LR, Moffett JW, Devol AH, Armbrust EV, Stahl DA, Ingalls AE. Two distinct pools of B12 analogs reveal community interdependencies in the ocean. Proceedings of the National Academy of Sciences of the United States of America. PMID 28028206 DOI: 10.1073/Pnas.1608462114  0.68
2016 Hosseinzadeh P, Tian S, Marshall NM, Hemp J, Mullen T, Nilges MJ, Gao YG, Robinson H, Stahl DA, Gennis RB, Lu Y. A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site. Journal of the American Chemical Society. PMID 27120678 DOI: 10.1021/Jacs.5B13128  1
2015 Bertagnolli AD, McCalmont D, Meinhardt KA, Fransen SC, Strand S, Brown S, Stahl DA. Agricultural land usage transforms nitrifier population ecology. Environmental Microbiology. PMID 26526405 DOI: 10.1111/1462-2920.13114  1
2015 Qin W, Carlson LT, Armbrust EV, Devol AH, Moffett JW, Stahl DA, Ingalls AE. Confounding effects of oxygen and temperature on the TEX86 signature of marine Thaumarchaeota. Proceedings of the National Academy of Sciences of the United States of America. 112: 10979-84. PMID 26283385 DOI: 10.1073/Pnas.1501568112  1
2015 Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. The Isme Journal. PMID 25848870 DOI: 10.1038/Ismej.2015.45  1
2015 Urakawa H, Garcia JC, Nielsen JL, Le VQ, Kozlowski JA, Stein LY, Lim CK, Pommerening-Röser A, Martens-Habbena W, Stahl DA, Klotz MG. Nitrosospira lacus sp. nov., a psychrotolerant, ammonia-oxidizing bacterium from sandy lake sediment. International Journal of Systematic and Evolutionary Microbiology. 65: 242-50. PMID 25336720 DOI: 10.1099/Ijs.0.070789-0  1
2014 Martens-Habbena W, Qin W, Horak RE, Urakawa H, Schauer AJ, Moffett JW, Armbrust EV, Ingalls AE, Devol AH, Stahl DA. The production of nitric oxide by marine ammonia-oxidizing archaea and inhibition of archaeal ammonia oxidation by a nitric oxide scavenger. Environmental Microbiology. PMID 25420929 DOI: 10.1111/1462-2920.12677  1
2014 Heal KR, Carlson LT, Devol AH, Armbrust EV, Moffett JW, Stahl DA, Ingalls AE. Determination of four forms of vitamin B12 and other B vitamins in seawater by liquid chromatography/tandem mass spectrometry. Rapid Communications in Mass Spectrometry : Rcm. 28: 2398-404. PMID 25303468 DOI: 10.1002/Rcm.7040  1
2014 Hillesland KL, Lim S, Flowers JJ, Turkarslan S, Pinel N, Zane GM, Elliott N, Qin Y, Wu L, Baliga NS, Zhou J, Wall JD, Stahl DA. Erosion of functional independence early in the evolution of a microbial mutualism. Proceedings of the National Academy of Sciences of the United States of America. 111: 14822-7. PMID 25267659 DOI: 10.1073/Pnas.1407986111  1
2014 Chong CS, Sabir DK, Lorenz A, Bontemps C, Andeer P, Stahl DA, Strand SE, Rylott EL, Bruce NC. Analysis of the xplAB-containing gene cluster involved in the bacterial degradation of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine. Applied and Environmental Microbiology. 80: 6601-10. PMID 25128343 DOI: 10.1128/Aem.01818-14  1
2014 Qin W, Amin SA, Martens-Habbena W, Walker CB, Urakawa H, Devol AH, Ingalls AE, Moffett JW, Armbrust EV, Stahl DA. Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation. Proceedings of the National Academy of Sciences of the United States of America. 111: 12504-9. PMID 25114236 DOI: 10.1073/Pnas.1324115111  1
2014 Könneke M, Schubert DM, Brown PC, Hügler M, Standfest S, Schwander T, Schada von Borzyskowski L, Erb TJ, Stahl DA, Berg IA. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proceedings of the National Academy of Sciences of the United States of America. 111: 8239-44. PMID 24843170 DOI: 10.1073/Pnas.1402028111  1
2014 Vajrala N, Bottomley PJ, Stahl DA, Arp DJ, Sayavedra-Soto LA. Cycloheximide prevents the de novo polypeptide synthesis required to recover from acetylene inhibition in Nitrosopumilus maritimus. Fems Microbiology Ecology. 88: 495-502. PMID 24606542 DOI: 10.1111/1574-6941.12316  1
2014 Gorman-Lewis D, Martens-Habbena W, Stahl DA. Thermodynamic characterization of proton-ionizable functional groups on the cell surfaces of ammonia-oxidizing bacteria and archaea. Geobiology. 12: 157-71. PMID 24589203 DOI: 10.1111/Gbi.12075  1
2014 Zhou J, Deng Y, Zhang P, Xue K, Liang Y, Van Nostrand JD, Yang Y, He Z, Wu L, Stahl DA, Hazen TC, Tiedje JM, Arkin AP. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem. Proceedings of the National Academy of Sciences of the United States of America. 111: E836-45. PMID 24550501 DOI: 10.1073/Pnas.1324044111  1
2014 Meyer B, Kuehl JV, Price MN, Ray J, Deutschbauer AM, Arkin AP, Stahl DA. The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environmental Microbiology. 16: 3463-86. PMID 24447568 DOI: 10.1111/1462-2920.12405  1
2014 Urakawa H, Martens-Habbena W, Huguet C, de la Torre JR, Ingalls AE, Devol AH, Stahl DA. Ammonia availability shapes the seasonal distribution and activity of archaeal and bacterial ammonia oxidizers in the Puget Sound Estuary Limnology and Oceanography. 59: 1321-1335. DOI: 10.4319/Lo.2014.59.4.1321  1
2014 Jacquot JE, Horak REA, Amin SA, Devol AH, Ingalls AE, Armbrust EV, Stahl DA, Moffett JW. Assessment of the potential for copper limitation of ammonia oxidation by Archaea in a dynamic estuary Marine Chemistry. 162: 37-49. DOI: 10.1016/J.Marchem.2014.02.002  1
2013 Nakagawa T, Stahl DA. Transcriptional response of the archaeal ammonia oxidizer Nitrosopumilus maritimus to low and environmentally relevant ammonia concentrations. Applied and Environmental Microbiology. 79: 6911-6. PMID 23995944 DOI: 10.1128/Aem.02028-13  1
2013 Pelve EA, Martens-Habbena W, Stahl DA, Bernander R. Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons. Molecular Microbiology. 90: 538-50. PMID 23991938 DOI: 10.1111/Mmi.12382  1
2013 Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. Journal of Bacteriology. 195: 4900-14. PMID 23974031 DOI: 10.1128/Jb.00504-13  1
2013 Andeer P, Stahl DA, Lillis L, Strand SE. Identification of microbial populations assimilating nitrogen from RDX in munitions contaminated military training range soils by high sensitivity stable isotope probing. Environmental Science & Technology. 47: 10356-63. PMID 23909596 DOI: 10.1021/Es401729C  1
2013 Krumholz LR, Wang L, Beck DA, Wang T, Hackett M, Mooney B, Juba TR, McInerney MJ, Meyer B, Wall JD, Stahl DA. Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis. Microbiology (Reading, England). 159: 2162-8. PMID 23842468 DOI: 10.1099/Mic.0.063818-0  1
2013 Kang S, Van Nostrand JD, Gough HL, He Z, Hazen TC, Stahl DA, Zhou J. Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments. Fems Microbiology Ecology. 86: 200-14. PMID 23710534 DOI: 10.1111/1574-6941.12152  1
2013 Horak RE, Qin W, Schauer AJ, Armbrust EV, Ingalls AE, Moffett JW, Stahl DA, Devol AH. Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea. The Isme Journal. 7: 2023-33. PMID 23657360 DOI: 10.1038/Ismej.2013.75  1
2013 Zhou A, Baidoo E, He Z, Mukhopadhyay A, Baumohl JK, Benke P, Joachimiak MP, Xie M, Song R, Arkin AP, Hazen TC, Keasling JD, Wall JD, Stahl DA, Zhou J. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution. The Isme Journal. 7: 1790-802. PMID 23575373 DOI: 10.1038/Ismej.2013.60  1
2013 Vajrala N, Martens-Habbena W, Sayavedra-Soto LA, Schauer A, Bottomley PJ, Stahl DA, Arp DJ. Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea. Proceedings of the National Academy of Sciences of the United States of America. 110: 1006-11. PMID 23277575 DOI: 10.1073/Pnas.1214272110  1
2013 Meyer B, Kuehl J, Deutschbauer AM, Price MN, Arkin AP, Stahl DA. Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. Journal of Bacteriology. 195: 990-1004. PMID 23264581 DOI: 10.1128/Jb.01959-12  1
2013 Amin SA, Moffett JW, Martens-Habbena W, Jacquot JE, Han Y, Devol A, Ingalls AE, Stahl DA, Armbrust EV. Copper requirements of the ammonia-oxidizing archaeon Nitrosopumilus maritimus SCM1 and implications for nitrification in the marine environment Limnology and Oceanography. 58: 2037-2045. DOI: 10.4319/Lo.2013.58.6.2037  1
2012 Yan J, Haaijer SC, Op den Camp HJ, van Niftrik L, Stahl DA, Könneke M, Rush D, Sinninghe Damsté JS, Hu YY, Jetten MS. Mimicking the oxygen minimum zones: stimulating interaction of aerobic archaeal and anaerobic bacterial ammonia oxidizers in a laboratory-scale model system. Environmental Microbiology. 14: 3146-58. PMID 23057688 DOI: 10.1111/J.1462-2920.2012.02894.X  1
2012 Stahl DA, de la Torre JR. Physiology and diversity of ammonia-oxidizing archaea. Annual Review of Microbiology. 66: 83-101. PMID 22994489 DOI: 10.1146/Annurev-Micro-092611-150128  1
2012 Metcalf WW, Griffin BM, Cicchillo RM, Gao J, Janga SC, Cooke HA, Circello BT, Evans BS, Martens-Habbena W, Stahl DA, van der Donk WA. Synthesis of methylphosphonic acid by marine microbes: a source for methane in the aerobic ocean. Science (New York, N.Y.). 337: 1104-7. PMID 22936780 DOI: 10.1126/Science.1219875  1
2012 Rajeev L, Hillesland KL, Zane GM, Zhou A, Joachimiak MP, He Z, Zhou J, Arkin AP, Wall JD, Stahl DA. Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. Journal of Bacteriology. 194: 5783-93. PMID 22904289 DOI: 10.1128/Jb.00749-12  1
2012 Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A, Stahl DA. Functional responses of methanogenic archaea to syntrophic growth. The Isme Journal. 6: 2045-55. PMID 22739494 DOI: 10.1038/Ismej.2012.60  1
2012 Berube PM, Stahl DA. The divergent AmoC3 subunit of ammonia monooxygenase functions as part of a stress response system in Nitrosomonas europaea. Journal of Bacteriology. 194: 3448-56. PMID 22544266 DOI: 10.1128/Jb.00133-12  1
2012 Kjeldsen KU, Bataillon T, Pinel N, De Mita S, Lund MB, Panitz F, Bendixen C, Stahl DA, Schramm A. Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms. Genome Biology and Evolution. 4: 307-15. PMID 22333491 DOI: 10.1093/Gbe/Evs014  1
2012 Dulla GF, Go RA, Stahl DA, Davidson SK. Verminephrobacter eiseniae type IV pili and flagella are required to colonize earthworm nephridia. The Isme Journal. 6: 1166-75. PMID 22170422 DOI: 10.1038/ismej.2011.183  1
2012 Merbt SN, Stahl DA, Casamayor EO, Martí E, Nicol GW, Prosser JI. Differential photoinhibition of bacterial and archaeal ammonia oxidation. Fems Microbiology Letters. 327: 41-6. PMID 22093004 DOI: 10.1111/J.1574-6968.2011.02457.X  1
2012 Andeer P, Strand SE, Stahl DA. High-sensitivity stable-isotope probing by a quantitative terminal restriction fragment length polymorphism protocol. Applied and Environmental Microbiology. 78: 163-9. PMID 22038597 DOI: 10.1128/Aem.05973-11  1
2012 Stahl DA, Flowers JJ, Hullar M, Davidson S. Structure and function of microbial communities The Prokaryotes: Prokaryotic Communities and Ecophysiology. 3-30. DOI: 10.1007/978-3-642-30123-0_34  1
2011 Pelve EA, LindÃ¥s AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R. Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus. Molecular Microbiology. 82: 555-66. PMID 21923770 DOI: 10.1111/J.1365-2958.2011.07834.X  1
2011 Li X, McInerney MJ, Stahl DA, Krumholz LR. Metabolism of H2 by Desulfovibrio alaskensis G20 during syntrophic growth on lactate. Microbiology (Reading, England). 157: 2912-21. PMID 21798981 DOI: 10.1099/Mic.0.051284-0  1
2011 Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP. How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nature Reviews. Microbiology. 9: 452-66. PMID 21572460 DOI: 10.1038/Nrmicro2575  1
2011 Martens-Habbena W, Stahl DA. Nitrogen metabolism and kinetics of ammonia-oxidizing archaea. Methods in Enzymology. 496: 465-87. PMID 21514476 DOI: 10.1016/B978-0-12-386489-5.00019-1  1
2011 Wang W, Kinkel T, Martens-Habbena W, Stahl DA, Fang FC, Hansen EJ. The Moraxella catarrhalis nitric oxide reductase is essential for nitric oxide detoxification. Journal of Bacteriology. 193: 2804-13. PMID 21441505 DOI: 10.1128/Jb.00139-11  1
2011 Gough HL, Stahl DA. Microbial community structures in anoxic freshwater lake sediment along a metal contamination gradient. The Isme Journal. 5: 543-58. PMID 20811473 DOI: 10.1038/Ismej.2010.132  1
2011 Hillesland KL, Stahl DA, Harcombe W. Measuring the costs of microbial mutualism Microbe. 6: 427-434. DOI: 10.1128/Microbe.6.427.1  1
2010 Davidson SK, Powell RJ, Stahl DA. Transmission of a bacterial consortium in Eisenia fetida egg capsules. Environmental Microbiology. 12: 2277-88. PMID 21966919 DOI: 10.1111/J.1462-2920.2010.02231.X  1
2010 Lund MB, Davidson SK, Holmstrup M, James S, Kjeldsen KU, Stahl DA, Schramm A. Diversity and host specificity of the Verminephrobacter-earthworm symbiosis. Environmental Microbiology. 12: 2142-51. PMID 21966909 DOI: 10.1111/j.1462-2920.2009.02084.x  1
2010 Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends in Microbiology. 18: 331-40. PMID 20598889 DOI: 10.1016/J.Tim.2010.06.003  1
2010 Zhou A, He Z, Redding-Johanson AM, Mukhopadhyay A, Hemme CL, Joachimiak MP, Luo F, Deng Y, Bender KS, He Q, Keasling JD, Stahl DA, Fields MW, Hazen TC, Arkin AP, et al. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environmental Microbiology. 12: 2645-57. PMID 20482586 DOI: 10.1111/J.1462-2920.2010.02234.X  1
2010 He Q, He Z, Joyner DC, Joachimiak M, Price MN, Yang ZK, Yen HC, Hemme CL, Chen W, Fields MM, Stahl DA, Keasling JD, Keller M, Arkin AP, Hazen TC, et al. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris. The Isme Journal. 4: 1386-97. PMID 20445634 DOI: 10.1038/Ismej.2010.59  1
2010 Walker CB, de la Torre JR, Klotz MG, Urakawa H, Pinel N, Arp DJ, Brochier-Armanet C, Chain PS, Chan PP, Gollabgir A, Hemp J, Hügler M, Karr EA, Könneke M, Shin M, ... ... Stahl DA, et al. Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proceedings of the National Academy of Sciences of the United States of America. 107: 8818-23. PMID 20421470 DOI: 10.1073/Pnas.0913533107  1
2010 Hillesland KL, Stahl DA. Rapid evolution of stability and productivity at the origin of a microbial mutualism. Proceedings of the National Academy of Sciences of the United States of America. 107: 2124-9. PMID 20133857 DOI: 10.1073/Pnas.0908456107  1
2010 Urakawa H, Martens-Habbena W, Stahl DA. High abundance of ammonia-oxidizing Archaea in coastal waters, determined using a modified DNA extraction method. Applied and Environmental Microbiology. 76: 2129-35. PMID 20118363 DOI: 10.1128/Aem.02692-09  1
2010 Hoffman LR, Richardson AR, Houston LS, Kulasekara HD, Martens-Habbena W, Klausen M, Burns JL, Stahl DA, Hassett DJ, Fang FC, Miller SI. Nutrient availability as a mechanism for selection of antibiotic tolerant Pseudomonas aeruginosa within the CF airway. Plos Pathogens. 6: e1000712. PMID 20072604 DOI: 10.1371/Journal.Ppat.1000712  1
2010 Bernhard AE, Landry ZC, Blevins A, de la Torre JR, Giblin AE, Stahl DA. Abundance of ammonia-oxidizing archaea and bacteria along an estuarine salinity gradient in relation to potential nitrification rates. Applied and Environmental Microbiology. 76: 1285-9. PMID 20038706 DOI: 10.1128/Aem.02018-09  1
2010 He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Applied and Environmental Microbiology. 76: 1574-86. PMID 20038696 DOI: 10.1128/Aem.02141-09  1
2010 Huguet C, Martens-Habbena W, Urakawa H, Stahl DA, Ingalls AE. Comparison of extraction methods for quantitative analysis of core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs) in environmental samples Limnology and Oceanography: Methods. 8: 127-145. DOI: 10.4319/Lom.2010.8.127  1
2010 Huguet C, Urakawa H, Martens-Habbena W, Truxal L, Stahl DA, Ingalls AE. Changes in intact membrane lipid content of archaeal cells as an indication of metabolic status Organic Geochemistry. 41: 930-934. DOI: 10.1016/J.Orggeochem.2010.04.012  1
2009 Kalyuhznaya MG, Martens-Habbena W, Wang T, Hackett M, Stolyar SM, Stahl DA, Lidstrom ME, Chistoserdova L. Methylophilaceae link methanol oxidation to denitrification in freshwater lake sediment as suggested by stable isotope probing and pure culture analysis. Environmental Microbiology Reports. 1: 385-92. PMID 23765891 DOI: 10.1111/J.1758-2229.2009.00046.X  1
2009 Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature. 461: 976-9. PMID 19794413 DOI: 10.1038/Nature08465  1
2009 Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HC, Zhou J, Wall JD, Hazen TC, Arkin AP, Stahl DA. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environmental Microbiology. 11: 2244-52. PMID 19737303 DOI: 10.1111/J.1462-2920.2009.01946.X  1
2009 Ziemer CJ, Kerr BJ, Trabue SL, Stein H, Stahl DA, Davidson SK. Dietary protein and cellulose effects on chemical and microbial characteristics of Swine feces and stored manure. Journal of Environmental Quality. 38: 2138-46. PMID 19704156 DOI: 10.2134/Jeq2008.0039  1
2009 Walker CB, He Z, Yang ZK, Ringbauer JA, He Q, Zhou J, Voordouw G, Wall JD, Arkin AP, Hazen TC, Stolyar S, Stahl DA. The electron transfer system of syntrophically grown Desulfovibrio vulgaris. Journal of Bacteriology. 191: 5793-801. PMID 19581361 DOI: 10.1128/Jb.00356-09  1
2009 Andeer PF, Stahl DA, Bruce NC, Strand SE. Lateral transfer of genes for hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation. Applied and Environmental Microbiology. 75: 3258-62. PMID 19270122 DOI: 10.1128/Aem.02396-08  1
2009 Dillon JG, Miller S, Bebout B, Hullar M, Pinel N, Stahl DA. Spatial and temporal variability in a stratified hypersaline microbial mat community. Fems Microbiology Ecology. 68: 46-58. PMID 19175677 DOI: 10.1111/J.1574-6941.2009.00647.X  1
2008 Wang W, Richardson AR, Martens-Habbena W, Stahl DA, Fang FC, Hansen EJ. Identification of a repressor of a truncated denitrification pathway in Moraxella catarrhalis. Journal of Bacteriology. 190: 7762-72. PMID 18820017 DOI: 10.1128/Jb.01032-08  1
2008 Pinel N, Davidson SK, Stahl DA. Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny). International Journal of Systematic and Evolutionary Microbiology. 58: 2147-57. PMID 18768621 DOI: 10.1099/ijs.0.65174-0  1
2008 Findlay RH, Yeates C, Hullar MA, Stahl DA, Kaplan LA. Biome-level biogeography of streambed microbiota. Applied and Environmental Microbiology. 74: 3014-21. PMID 18378660 DOI: 10.1128/Aem.01809-07  1
2008 Schouten S, Hopmans EC, Baas M, Boumann H, Standfest S, Könneke M, Stahl DA, Sinninghe Damsté JS. Intact membrane lipids of "Candidatus Nitrosopumilus maritimus," a cultivated representative of the cosmopolitan mesophilic group I Crenarchaeota. Applied and Environmental Microbiology. 74: 2433-40. PMID 18296531 DOI: 10.1128/Aem.01709-07  1
2008 Davidson SK, Stahl DA. Selective recruitment of bacteria during embryogenesis of an earthworm. The Isme Journal. 2: 510-8. PMID 18273064 DOI: 10.1038/Ismej.2008.16  1
2008 de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environmental Microbiology. 10: 810-8. PMID 18205821 DOI: 10.1111/J.1462-2920.2007.01506.X  1
2008 Bavykin SG, Mikhailovich VM, Zakharyev VM, Lysov YP, Kelly JJ, Alferov OS, Gavin IM, Kukhtin AV, Jackman J, Stahl DA, Chandler D, Mirzabekov AD. Discrimination of Bacillus anthracis and closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microarray. Chemico-Biological Interactions. 171: 212-35. PMID 17950718 DOI: 10.1016/j.cbi.2007.09.002  1
2008 Gough HL, Dahl AL, Tribou E, Noble PA, Gaillard JF, Stahl DA. Elevated sulfate reduction in metal-contaminated freshwater lake sediments Journal of Geophysical Research: Biogeosciences. 113. DOI: 10.1029/2008Jg000738  1
2008 Gough HL, Dahl AL, Nolan MA, Gaillard JF, Stahl DA. Metal impacts on microbial biomass in the anoxic sediments of a contaminated lake Journal of Geophysical Research: Biogeosciences. 113. DOI: 10.1029/2007Jg000566  1
2007 Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, Stahl DA. Response of Desulfovibrio vulgaris to alkaline stress. Journal of Bacteriology. 189: 8944-52. PMID 17921288 DOI: 10.1128/Jb.00284-07  1
2007 Dillon JG, Fishbain S, Miller SR, Bebout BM, Habicht KS, Webb SM, Stahl DA. High rates of sulfate reduction in a low-sulfate hot spring microbial mat are driven by a low level of diversity of sulfate-respiring microorganisms. Applied and Environmental Microbiology. 73: 5218-26. PMID 17575000 DOI: 10.1128/Aem.00357-07  1
2007 Bernhard AE, Tucker J, Giblin AE, Stahl DA. Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient. Environmental Microbiology. 9: 1439-47. PMID 17504481 DOI: 10.1111/J.1462-2920.2007.01260.X  1
2007 Starke EM, Smoot JC, Wu JH, Liu WT, Chandler D, Stahl DA. Saliva-based diagnostics using 16S rRNA microarrays and microfluidics. Annals of the New York Academy of Sciences. 1098: 345-61. PMID 17435141 DOI: 10.1196/Annals.1384.007  1
2007 Berube PM, Samudrala R, Stahl DA. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. Journal of Bacteriology. 189: 3935-44. PMID 17384196 DOI: 10.1128/Jb.01861-06  1
2007 Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA. Metabolic modeling of a mutualistic microbial community. Molecular Systems Biology. 3: 92. PMID 17353934 DOI: 10.1038/Msb4100131  1
2007 Siripong S, Kelly JJ, Stahl DA, Rittmann BE. Influence of grid placement on melting profiles obtained from gel-pad microarrays [2] Environmental Microbiology. 9: 1866-1867. DOI: 10.1111/j.1462-2920.2007.01297.x  1
2007 Eyers L, Smoot JC, Stahl DA. Response to comment on "discrimination of shifts in a soil microbial community associated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays" Environmental Science and Technology. 41: 1799-1800. DOI: 10.1021/es0629514  1
2007 Stahl DA, Loy A, Wagner M. Molecular strategies for studies of natural populations of sulphate-reducing microorganisms Sulphate-Reducing Bacteria: Environmental and Engineered Systems. 39-116. DOI: 10.1017/CBO9780511541490.003  1
2006 Hazen TC, Timmis K, Stahl D, Delong E, Wagner M. This issue of Environmental Microbiology is dedicated to the memory of David. C. White. Environmental Microbiology. 8: 2059-61. PMID 17107546 DOI: 10.1111/j.1462-2920.2006.01192.x  1
2006 Stahl DA, Davidson SK. Genomics: blueprints for partnerships. Nature. 443: 925-7. PMID 17073006 DOI: 10.1038/Nature05208  1
2006 Eyers L, Smoot JC, Smoot LM, Bugli C, Urakawa H, McMurry Z, Siripong S, El-Fantroussi S, Lambert P, Agathos SN, Stahl DA. Discrimination of shifts in a soil microbial community associated with TNT-contamination using a functional ANOVA of 16S rRNA hybridized to oligonucleotide microarrays. Environmental Science & Technology. 40: 5867-73. PMID 17051772 DOI: 10.1021/Es0609093  1
2006 Walker CB, Stolyar SS, Pinel N, Yen HC, He Z, Zhou J, Wall JD, Stahl DA. Recovery of temperate Desulfovibrio vulgaris bacteriophage using a novel host strain. Environmental Microbiology. 8: 1950-9. PMID 17014494 DOI: 10.1111/J.1462-2920.2006.01075.X  1
2006 Starke EM, Smoot JC, Smoot LM, Liu WT, Chandler DP, Lee HH, Stahl DA. Technology development to explore the relationship between oral health and the oral microbial community. Bmc Oral Health. 6: S10. PMID 16934111 DOI: 10.1186/1472-6831-6-S1-S10  1
2006 Lee HH, Smoot J, McMurray Z, Stahl DA, Yager P. Recirculating flow accelerates DNA microarray hybridization in a microfluidic device. Lab On a Chip. 6: 1163-70. PMID 16929395 DOI: 10.1039/B605507A  1
2006 Siripong S, Kelly JJ, Stahl DA, Rittmann BE. Impact of prehybridization PCR amplification on microarray detection of nitrifying bacteria in wastewater treatment plant samples. Environmental Microbiology. 8: 1564-74. PMID 16913917 DOI: 10.1111/J.1462-2920.2006.01047.X  1
2006 Hazen TC, Stahl DA. Using the stress response to monitor process control: pathways to more effective bioremediation. Current Opinion in Biotechnology. 17: 285-90. PMID 16616486 DOI: 10.1016/J.Copbio.2006.03.004  1
2006 Davidson SK, Stahl DA. Transmission of nephridial bacteria of the earthworm Eisenia fetida. Applied and Environmental Microbiology. 72: 769-75. PMID 16391117 DOI: 10.1128/AEM.72.1.769-775.2006  1
2006 Hullar MA, Kaplan LA, Stahl DA. Recurring seasonal dynamics of microbial communities in stream habitats. Applied and Environmental Microbiology. 72: 713-22. PMID 16391111 DOI: 10.1128/Aem.72.1.713-722.2006  1
2006 Becker JG, Berardesco G, Rittmann BE, Stahl DA. Effects of endogenous substrates on adaptation of anaerobic microbial communities to 3-chlorobenzoate. Applied and Environmental Microbiology. 72: 449-56. PMID 16391077 DOI: 10.1128/Aem.72.1.449-456.2006  1
2006 Stahl DA, Wagner M. The knowledge explosion in environmental microbiology offers new opportunities in biotechnology Current Opinion in Biotechnology. 17: 227-228. DOI: 10.1016/J.Copbio.2006.05.010  1
2005 Wagner M, Loy A, Klein M, Lee N, Ramsing NB, Stahl DA, Friedrich MW. Functional marker genes for identification of sulfate-reducing prokaryotes. Methods in Enzymology. 397: 469-89. PMID 16260310 DOI: 10.1016/S0076-6879(05)97029-8  1
2005 Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 437: 543-6. PMID 16177789 DOI: 10.1038/Nature03911  1
2005 Bernhard AE, Donn T, Giblin AE, Stahl DA. Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. Environmental Microbiology. 7: 1289-97. PMID 16104852 DOI: 10.1111/J.1462-2920.2005.00808.X  1
2005 Kelly JJ, Siripong S, McCormack J, Janus LR, Urakawa H, El Fantroussi S, Noble PA, Sappelsa L, Rittmann BE, Stahl DA. DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Research. 39: 3229-38. PMID 16009395 DOI: 10.1016/J.Watres.2005.05.044  1
2005 Smoot LM, Smoot JC, Smidt H, Noble PA, Könneke M, McMurry ZA, Stahl DA. DNA microarrays as salivary diagnostic tools for characterizing the oral cavity's microbial community. Advances in Dental Research. 18: 6-11. PMID 15998937 DOI: 10.1177/154407370501800103  1
2005 Urakawa H, Dubilier N, Fujiwara Y, Cunningham DE, Kojima S, Stahl DA. Hydrothermal vent gastropods from the same family (Provannidae) harbour epsilon- and gamma-proteobacterial endosymbionts. Environmental Microbiology. 7: 750-4. PMID 15819856 DOI: 10.1111/J.1462-2920.2005.00753.X  1
2005 Zverlov V, Klein M, Lücker S, Friedrich MW, Kellermann J, Stahl DA, Loy A, Wagner M. Lateral gene transfer of dissimilatory (bi)sulfite reductase revisited. Journal of Bacteriology. 187: 2203-8. PMID 15743970 DOI: 10.1128/Jb.187.6.2203-2208.2005  1
2005 Becker JG, Berardesco G, Rittmann BE, Stahl DA. The role of syntrophic associations in sustaining anaerobic mineralization of chlorinated organic compounds. Environmental Health Perspectives. 113: 310-6. PMID 15743720 DOI: 10.1289/Ehp.6933  1
2004 Bavykin SG, Lysov YP, Zakhariev V, Kelly JJ, Jackman J, Stahl DA, Cherni A. Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms. Journal of Clinical Microbiology. 42: 3711-30. PMID 15297521 DOI: 10.1128/Jcm.42.8.3711-3730.2004  1
2004 Stahl DA. High-throughput techniques for analyzing complex bacterial communities. Advances in Experimental Medicine and Biology. 547: 5-17. PMID 15230089 DOI: 10.1007/978-1-4419-8861-4_2  1
2004 Thomsen U, Thamdrup B, Stahl DA, Canfield DE. Pathways of organic carbon oxidation in a deep lacustrine sediment, Lake Michigan Limnology and Oceanography. 49: 2046-2057. DOI: 10.4319/Lo.2004.49.6.2046  1
2003 Schramm A, Davidson SK, Dodsworth JA, Drake HL, Stahl DA, Dubilier N. Acidovorax-like symbionts in the nephridia of earthworms. Environmental Microbiology. 5: 804-9. PMID 12919416 DOI: 10.1046/J.1462-2920.2003.00474.X  1
2003 Fishbain S, Dillon JG, Gough HL, Stahl DA. Linkage of high rates of sulfate reduction in Yellowstone hot springs to unique sequence types in the dissimilatory sulfate respiration pathway. Applied and Environmental Microbiology. 69: 3663-7. PMID 12788778 DOI: 10.1128/Aem.69.6.3663-3667.2003  1
2003 Urakawa H, El Fantroussi S, Smidt H, Smoot JC, Tribou EH, Kelly JJ, Noble PA, Stahl DA. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Applied and Environmental Microbiology. 69: 2848-56. PMID 12732557 DOI: 10.1128/Aem.69.5.2848-2856.2003  1
2003 Dhillon A, Teske A, Dillon J, Stahl DA, Sogin ML. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Applied and Environmental Microbiology. 69: 2765-72. PMID 12732547 DOI: 10.1128/Aem.69.5.2765-2772.2003  1
2003 El Fantroussi S, Urakawa H, Bernhard AE, Kelly JJ, Noble PA, Smidt H, Yershov GM, Stahl DA. Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays. Applied and Environmental Microbiology. 69: 2377-82. PMID 12676724 DOI: 10.1128/Aem.69.4.2377-2382.2003  1
2003 Baker BJ, Moser DP, MacGregor BJ, Fishbain S, Wagner M, Fry NK, Jackson B, Speolstra N, Loos S, Takai K, Lollar BS, Fredrickson J, Balkwill D, Onstott TC, Wimpee CF, ... Stahl DA, et al. Related assemblages of sulphate-reducing bacteria associated with ultradeep gold mines of South Africa and deep basalt aquifers of Washington State. Environmental Microbiology. 5: 267-77. PMID 12662174 DOI: 10.1046/J.1462-2920.2003.00408.X  1
2003 Gough HL, Stahl DA. Optimization of direct cell counting in sediment. Journal of Microbiological Methods. 52: 39-46. PMID 12401225 DOI: 10.1016/S0167-7012(02)00135-5  1
2002 Schramm A, Fuchs BM, Nielsen JL, Tonolla M, Stahl DA. Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environmental Microbiology. 4: 713-20. PMID 12460279 DOI: 10.1046/J.1462-2920.2002.00364.X  1
2002 Stahl DA, Fishbain S, Klein M, Baker BJ, Wagner M. Origins and diversification of sulfate-respiring microorganisms. Antonie Van Leeuwenhoek. 81: 189-95. PMID 12448717 DOI: 10.1023/A:1020506415921  1
2002 Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA. Persistence and functional impact of a microbial inoculant on native microbial community structure, nutrient digestion and fermentation characteristics in a rumen model. Systematic and Applied Microbiology. 25: 416-22. PMID 12421079 DOI: 10.1078/0723-2020-00125  1
2002 Davis JW, Odom JM, Deweerd KA, Stahl DA, Fishbain SS, West RJ, Klecka GM, DeCarolis JG. Natural attenuation of chlorinated solvents at Area 6, Dover Air Force Base: characterization of microbial community structure. Journal of Contaminant Hydrology. 57: 41-59. PMID 12143992 DOI: 10.1016/S0169-7722(01)00217-0  1
2002 Koizumi Y, Kelly JJ, Nakagawa T, Urakawa H, El-Fantroussi S, Al-Muzaini S, Fukui M, Urushigawa Y, Stahl DA. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Applied and Environmental Microbiology. 68: 3215-25. PMID 12088997 DOI: 10.1128/Aem.68.7.3215-3225.2002  1
2002 Abeysinghe DH, De Silva DG, Stahl DA, Rittmann BE. The effectiveness of bioaugmentation in nitrifying systems stressed by a washout condition and cold temperature. Water Environment Research : a Research Publication of the Water Environment Federation. 74: 187-99. PMID 12043976 DOI: 10.2175/106143002X139901  1
2002 Taillefert M, MacGregor BJ, Gaillard JF, Lienemann CP, Perret D, Stahl DA. Evidence for a dynamic cycle between Mn and Co in the water column of a stratified lake. Environmental Science & Technology. 36: 468-76. PMID 11871563 DOI: 10.1021/Es010915T  1
2002 Urakawa H, Noble PA, El Fantroussi S, Kelly JJ, Stahl DA. Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Applied and Environmental Microbiology. 68: 235-44. PMID 11772632 DOI: 10.1128/Aem.68.1.235-244.2002  1
2002 Stahl DA, El Fantroussi S, Urakawa H, Noble P, Smidt H, Smoot J, Kelly J. DNA microchip based microbial monitoring of environmental systems Sae Technical Papers. DOI: 10.4271/2002-01-2452  1
2001 Becker JG, Berardesco G, Rittmann BE, Stahl DA. Successional Changes in an Evolving Anaerobic Chlorophenol-Degrading Community Used to Infer Relationships between Population Structure and System-Level Processes Applied and Environmental Microbiology. 67: 5705-5714. PMID 11722926 DOI: 10.1128/Aem.67.12.5705-5714.2001  1
2001 Liu WT, Mirzabekov AD, Stahl DA. Optimization of an oligonucleotide microchip for microbial identification studies: A non-equilibrium dissociation approach Environmental Microbiology. 3: 619-629. PMID 11722542 DOI: 10.1046/J.1462-2920.2001.00233.X  1
2001 Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes Journal of Bacteriology. 183: 6028-6035. PMID 11567003 DOI: 10.1128/Jb.183.20.6028-6035.2001  1
2001 MacGregor BJ, Moser DP, Baker BJ, Alm EW, Maurer M, Nealson KH, Stahl DA. Seasonal and spatial variability in Lake Michigan sediment small-subunit rRNA concentrations. Applied and Environmental Microbiology. 67: 3908-22. PMID 11525985 DOI: 10.1128/Aem.67.9.3908-3922.2001  1
2001 Webb SM, Gaillard JF, Jackson BE, Stahl DA. An EXAFS study of zinc coordination in microbial cells. Journal of Synchrotron Radiation. 8: 943-5. PMID 11512987 DOI: 10.1107/S0909049500020975  1
2001 MacGregor BJ, Van Mooy B, Baker BJ, Mellon M, Moisander PH, Paerl HW, Zehr J, Hollander D, Stahl DA. Microbiological, molecular biological and stable isotopic evidence for nitrogen fixation in the open waters of Lake Michigan. Environmental Microbiology. 3: 205-19. PMID 11321537 DOI: 10.1046/J.1462-2920.2001.00180.X  1
2001 MacGregor BJ, Toze S, Alm EW, Sharp R, Ziemer CJ, Stahl DA. Distribution and abundance of Gram-positive bacteria in the environment: development of a group-specific probe. Journal of Microbiological Methods. 44: 193-203. PMID 11240041 DOI: 10.1016/S0167-7012(00)00243-8  1
2000 Caldwell DE, Colwell RR, Harayama S, Kjelleberg S, Givskov M, Molin S, Nielsen AT, Heydorn A, Tolker-Nielsen T, Sternberg C, Nealson K, Pace NR, Rainey P, Stackebrandt E, Tindall BJ, ... Stahl DA, et al. Crystal ball: leading scientists in the field of environmental microbiology consider the technical and conceptual developments that they believe will drive innovative research during the first years of the new millennium. Environmental Microbiology. 2: 3-10. PMID 11243260  1
2000 Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA. Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes. Environmental Microbiology. 2: 632-43. PMID 11214796 DOI: 10.1046/J.1462-2920.2000.00146.X  1
2000 Alm EW, Stahl DA. Critical factors influencing the recovery and integrity of rRNA extracted from environmental samples: use of an optimized protocol to measure depth-related biomass distribution in freshwater sediments. Journal of Microbiological Methods. 40: 153-62. PMID 10699671 DOI: 10.1016/S0167-7012(00)00120-2  1
2000 Stahl DA. Small instruments for the study of small life Environmental Microbiology. 2: 10.  1
2000 Webb SM, Gaillard JF, Nolan MA, Jackson BE, Stahl DA. An EXAFS study of zinc speciation in anaerobic microbes Acs Division of Environmental Chemistry, Preprints. 40: 326-328.  1
2000 Nolan MA, Jackson BE, Webb SM, Gaillard JF, Stahl DA. Electrochemical study of metal-microbe interactions Acs Division of Environmental Chemistry, Preprints. 40: 421-423.  1
1999 Sahm K, MacGregor BJ, Jørgensen BB, Stahl DA. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment Environmental Microbiology. 1: 65-74. PMID 11207719 DOI: 10.1046/J.1462-2920.1999.00007.X  1
1999 Becker JG, Stahl DA, Rittmann BE. Reductive dehalogenation and conversion of 2-chlorophenol to 3- chlorobenzoate in a methanogenic sediment community: Implications for predicting the environmental fate of chlorinated pollutants Applied and Environmental Microbiology. 65: 5169-5172. PMID 10543840 DOI: 10.1128/Aem.65.11.5169-5172.1999  1
1999 Minz D, Flax JL, Green SJ, Muyzer G, Cohen Y, Wagner M, Rittmann BE, Stahl DA. Diversity of sulfate-reducing bacteria in oxic and anoxic regions of a microbial mat characterized by comparative analysis of dissimilatory sulfite reductase genes Applied and Environmental Microbiology. 65: 4666-4671. PMID 10508104 DOI: 10.1128/Aem.65.10.4666-4671.1999  1
1999 Minz D, Fishbain S, Green SJ, Muyzer G, Cohen Y, Rittmann BE, Stahl DA. Unexpected population distribution in a microbial mat community: Sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia Applied and Environmental Microbiology. 65: 4659-4665. PMID 10508103 DOI: 10.1128/Aem.65.10.4659-4665.1999  1
1999 Vetriani C, Jannasch HW, Macgregor BJ, Stahl DA, Reysenbach AL. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments Applied and Environmental Microbiology. 65: 4375-4384. PMID 10508063 DOI: 10.1128/Aem.65.10.4375-4384.1999  1
1999 Nielsen AT, Liu WT, Filipe C, Grady L, Molin S, Stahl DA. Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor Applied and Environmental Microbiology. 65: 1251-1258. PMID 10049891 DOI: 10.1128/Aem.65.3.1251-1258.1999  1
1999 Berardesco G, Kelly J, Sappelsa L, Stahl DA. DNA microchip-based microbial montoring Sae Technical Papers. DOI: 10.4271/1999-01-2031  1
1999 Noguera DR, Pizarro G, Stahl DA, Rittmann BE. Simulation of multispecies biofilm development in three dimensions Water Science and Technology. 39: 123-130. DOI: 10.1016/S0273-1223(99)00159-6  1
1999 Rittmann BE, Pettis M, Reeves HW, Stahl DA. How biofilm clusters affect substrate flux and ecological selection Water Science and Technology. 39: 99-105. DOI: 10.1016/S0273-1223(99)00156-0  1
1999 Lazarova V, Bellahcen D, Manem J, Stahl DA, Rittmann BE. Influence of operating conditions on population dynamics in nitrifying biofilms Water Science and Technology. 39: 5-11. DOI: 10.1016/S0273-1223(99)00144-4  1
1999 Rittmann BE, Laspidou CS, Flax J, Stahl DA, Urbain V, Harduin H, Van Der Waarde JJ, Geurkink B, Henssen MJC, Brouwer H, Klapwijk A, Wetterauw M. Molecular and modeling analyses of the structure and function of nitrifying activated sludge Water Science and Technology. 39: 51-59. DOI: 10.1016/S0273-1223(98)00775-6  1
1998 McMahon KD, Stahl DA, Raskin L. A Comparison of the Use of In Vitro-Transcribed and Native rRNA for the Quantification of Microorganisms in the Environment. Microbial Ecology. 36: 362-371. PMID 9852515 DOI: 10.1007/S002489900122  1
1998 Wagner M, Roger AJ, Flax JL, Brusseau GA, Stahl DA. Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration Journal of Bacteriology. 180: 2975-2982. PMID 9603890 DOI: 10.1128/Jb.180.11.2975-2982.1998  1
1998 Sharp R, Ziemer CJ, Stern MD, Stahl DA. Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system Fems Microbiology Ecology. 26: 71-78. DOI: 10.1111/J.1574-6941.1998.Tb01563.X  1
1998 Urbain V, Mobarry B, De Silva V, Stahl DA, Rittmann BE, Manem J. Integration of performance, molecular biology and modeling to describe the activated sludge process Water Science and Technology. 37: 223-229. DOI: 10.1016/S0273-1223(98)00111-5  1
1998 McMahon KD, Stahl DA, Raskin L. A comparison of the use of in vitro-transcribed and native rRNA for the quantification of microorganisms in the environment Microbial Ecology. 36: 362-371. DOI: 10.1007/s002489900122  1
1998 Noguera DR, Brusseau GA, Rittmann BE, Stahl DA. A unified model describing the role of hydrogen in the growth of Desulfovibrio vulgaris under different environmental conditions Biotechnology and Bioengineering. 59: 732-746. DOI: 10.1002/(Sici)1097-0290(19980920)59:6<732::Aid-Bit10>3.0.Co;2-7  1
1997 Tuhela L, Robinson JB, Fishbain S, Stahl DA, Tuovinen OH. Phylogenetic and narG analysis of a Hyphomicrobium isolate Current Microbiology. 35: 244-248. PMID 9290067 DOI: 10.1007/S002849900247  1
1997 Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology Applied and Environmental Microbiology. 63: 2397-2402. PMID 9172361 DOI: 10.1128/Aem.63.6.2397-2402.1997  1
1997 Fry NK, Fredrickson JK, Fishbain S, Wagner M, Stahl DA. Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers Applied and Environmental Microbiology. 63: 1498-1504. PMID 9097447 DOI: 10.1128/Aem.63.4.1498-1504.1997  1
1997 MacGregor BJ, Moser DP, Alm EW, Nealson KH, Stahl DA. Crenarchaeota in Lake Michigan sediment. Applied and Environmental Microbiology. 63: 1178-81. PMID 9055434 DOI: 10.1128/Aem.63.3.1178-1181.1997  1
1997 Lin C, Raskin L, Stahl DA. Microbial community structure in gastrointestinal tracts of domestic animals: Comparative analyses using rRNA-targeted oligonucleotide probes Fems Microbiology Ecology. 22: 281-294. DOI: 10.1111/J.1574-6941.1997.Tb00380.X  1
1997 Nealson KH, Stahl DA. Microorganisms and biogeochemical cycles: What can we learn from layered microbial communities? Reviews in Mineralogy. 35: 30-34.  1
1996 Zheng D, Alm EW, Stahl DA, Raskin L. Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Applied and Environmental Microbiology. 62: 4504-13. PMID 8953722 DOI: 10.1128/Aem.62.12.4504-4513.1996  1
1996 Alm EW, Oerther DB, Larsen N, Stahl DA, Raskin L. The oligonucleotide probe database. Applied and Environmental Microbiology. 62: 3557-9. PMID 8837410 DOI: 10.1128/Aem.62.10.3557-3559.1996  1
1995 Rittmann BE, Smets BF, MacDonald JA, Stahl DA. Plasmid transfer for enhancing degradation capabilities Environmental Health Perspectives. 103: 113-115. PMID 8565897 DOI: 10.1289/Ehp.95103S4113  1
1995 Smets BF, Rittmann BE, Stahl DA. Quantification of the effect of substrate concentration on the conjugal transfer rate of the TOL plasmid in short term batch mating experiments Letters in Applied Microbiology. 21: 167-172. PMID 7576502 DOI: 10.1111/J.1472-765X.1995.Tb01033.X  1
1995 Ohashi A, Silva DGVd, Mobarry B, Manem JA, Stahl DA, Rittmann BE. Influence of substrate C/N ratio on the structure of multi-species biofilms consisting of nitrifiers and heterotrophs Water Science and Technology. 32: 75-84. DOI: 10.1016/0273-1223(96)00010-8  1
1995 Raskin L, Amann RI, Poulsen LK, Rittmann BE, Stahl DA. Use of ribosomal RNA-based molecular probes for characterization of complex microbial communities in anaerobic biofilms Water Science and Technology. 31: 261-272. DOI: 10.1016/0273-1223(95)00173-K  1
1994 Cornick NA, Jensen NS, Stahl DA, Hartman PA, Allison MJ. Lachnospira pectinoschiza sp. nov., an anaerobic pectinophile from the pig intestine International Journal of Systematic Bacteriology. 44: 87-93. PMID 8123565 DOI: 10.1099/00207713-44-1-87  1
1993 Smets BF, Rittmann BE, Stahl DA. The specific growth rate of Pseudomonas putida PAW1 influences the conjugal transfer rate of the TOL plasmid Applied and Environmental Microbiology. 59: 3430-3437. PMID 8250565 DOI: 10.1128/Aem.59.10.3430-3437.1993  1
1993 Poulsen LK, Ballard G, Stahl DA. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms Applied and Environmental Microbiology. 59: 1354-1360. PMID 7685999 DOI: 10.1128/Aem.59.5.1354-1360.1993  1
1993 Krumholz LR, Bryant MP, Brulla WJ, Vicini JL, Clark JH, Stahl DA. Proposal of Quinella ovalis gen. nov., sp. nov., based on phylogenetic analysis International Journal of Systematic Bacteriology. 43: 293-296. PMID 7684240 DOI: 10.1099/00207713-43-2-293  1
1992 Lane DJ, Harrison AP, Stahl D, Pace B, Giovannoni SJ, Olsen GJ, Pace NR. Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. Journal of Bacteriology. 174: 269-78. PMID 1729214 DOI: 10.1128/Jb.174.1.269-278.1992  1
1990 Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and Environmental Microbiology. 56: 1919-25. PMID 2200342 DOI: 10.1128/Aem.56.6.1919-1925.1990  1
1988 Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR, Stahl DA, Felbeck H. Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences Journal of Bacteriology. 170: 2506-2510. PMID 3286609 DOI: 10.1128/Jb.170.6.2506-2510.1988  1
1987 Romaniuk PJ, Zoltowska B, Trust TJ, Lane DJ, Olsen GJ, Pace NR, Stahl DA. Campylobacter pylori, the spiral bacterium associated with human gastritis, is not a true Campylobacter sp Journal of Bacteriology. 169: 2137-2141. PMID 3571163 DOI: 10.1128/Jb.169.5.2137-2141.1987  1
1986 Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA. Microbial ecology and evolution: a ribosomal RNA approach. Annual Review of Microbiology. 40: 337-65. PMID 2430518 DOI: 10.1146/Annurev.Mi.40.100186.002005  1
1986 Pace NR, Stahl DA, Lane DJ, Olsen GJ. The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences Advances in Microbial Ecology. 9: 1-55. DOI: 10.1007/978-1-4757-0611-6_1  1
1985 Lane DJ, Stahl DA, Olsen GJ, Heller DJ, Pace NR. Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S rRNA sequences. Journal of Bacteriology. 163: 75-81. PMID 3924899 DOI: 10.1128/Jb.163.1.75-81.1985  1
1985 Rogers MJ, Simmons J, Walker RT, Weisburg WG, Woese CR, Tanner RS, Robinson IM, Stahl DA, Olsen G, Leach RH. Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data Proceedings of the National Academy of Sciences of the United States of America. 82: 1160-1164. PMID 2579388 DOI: 10.1073/Pnas.82.4.1160  1
1985 Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proceedings of the National Academy of Sciences of the United States of America. 82: 6955-9. PMID 2413450 DOI: 10.1073/Pnas.82.20.6955  1
1985 Pierson BK, Giovannoni SJ, Stahl DA, Castenholz RW. Heliothrix oregonensis, gen. nov., sp. nov., a phototrophic filamentous gliding bacterium containing bacteriochlorophyll a Archives of Microbiology. 142: 164-167. PMID 2412519 DOI: 10.1007/Bf00447061  1
1985 Stahl DA, Lane DJ, Olsen GJ, Pace NR. Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences. Applied and Environmental Microbiology. 49: 1379-84. PMID 2409920 DOI: 10.1128/Aem.49.6.1379-1384.1985  1
1984 Stahl DA, Lane DJ, Olsen GJ, Pace NR. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science (New York, N.Y.). 224: 409-11. PMID 17741220 DOI: 10.1126/Science.224.4647.409  1
1984 Pace B, Stahl DA, Pace NR. The catalytic element of a ribosomal RNA-processing complex. The Journal of Biological Chemistry. 259: 11454-8. PMID 6432798  1
1984 Stahl DA, Pace B, Marsh T, Pace NR. The ribonucleoprotein substrate for a ribosomal RNA-processing nuclease. The Journal of Biological Chemistry. 259: 11448-53. PMID 6432797  1
1981 Noller HF, Kop J, Wheaton V, Brosius J, Gutell RR, Kopylov AM, Dohme F, Herr W, Stahl DA, Gupta R, Woese CR. Secondary structure model for 23S ribosomal RNA Nucleic Acids Research. 9: 6167-6189. PMID 7031608 DOI: 10.1093/Nar/9.22.6167  1
1981 Stahl DA, Luehrsent KR, Woese CR, Pace NR. An unusual 5S rRNA, from sulfolobus acidocaldarius, and its implications for a general 5S rRNA structure Nucleic Acids Research. 9: 6129-6138. PMID 6273825 DOI: 10.1093/Nar/9.22.6129  1
1980 Stahl DA, Meyhack B, Pace NR. Recognition of local nucleotide conformation in contrast to sequence by a rRNA processing endonuclease. Proceedings of the National Academy of Sciences of the United States of America. 77: 5644-8. PMID 6777771 DOI: 10.1073/Pnas.77.10.5644  1
1980 Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB, Blakemore R, Gupta R, Bonen L, Lewis BJ, ... Stahl DA, et al. The phylogeny of prokaryotes. Science (New York, N.Y.). 209: 457-63. PMID 6771870 DOI: 10.1126/Science.6771870  0.48
1980 Woese CR, Magrum LJ, Gupta R, Siegel RB, Stahl DA, Kop J, Crawford N, Brosius R, Gutell R, Hogan JJ, Noller HF. Secondary structure model for bacterial 16S ribosomal RNA: Phylogenetic, enzymatic and chemical evidence Nucleic Acids Research. 8: 2275-2294. PMID 6159576 DOI: 10.1093/Nar/8.10.2275  1
1979 Stahl DA, Walker TA, Meyhack B, Pace NR. Precursor-specific nucleotide sequences can govern RNA folding Cell. 18: 1133-1143. PMID 117902 DOI: 10.1016/0092-8674(79)90226-5  1
1976 Woese C, Sogin M, Stahl D, Lewis BJ, Bonen L. A comparison of the 16S ribosomal RNAs from mesophilic and thermophilic bacilli: some modifications in the Sanger method for RNA sequencing. Journal of Molecular Evolution. 7: 197-213. PMID 819656 DOI: 10.1007/Bf01731489  1
1975 Woese CR, Fox GE, Zablen L, Uchida T, Bonen L, Pechman K, Lewis BJ, Stahl D. Conservation of primary structure in 16S ribosomal RNA. Nature. 254: 83-6. PMID 1089909 DOI: 10.1038/254083A0  1
1975 Woese CR, Sogin ML, Bonen L, Stahl D. Sequence studies on 16S ribosomal RNA from a blue-green alga. Journal of Molecular Evolution. 4: 307-15. PMID 813006 DOI: 10.1007/Bf01732533  1
1975 Magrum L, Zablen L, Stahl D, Woese C. Corrections in the catalogue of oligonucleotides produced by digestion of Escherichia coli 16S rRNA with T1 RNase Nature. 257: 423-426. PMID 809718 DOI: 10.1038/257423A0  1
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